1
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Li F, Ma Z, Cai Y, Zhou J, Liu R. Optimizing diabetic kidney disease animal models: Insights from a meta-analytic approach. Animal Model Exp Med 2023; 6:433-451. [PMID: 37723622 PMCID: PMC10614131 DOI: 10.1002/ame2.12350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/12/2023] [Indexed: 09/20/2023] Open
Abstract
Diabetic kidney disease (DKD) is a prevalent complication of diabetes, often leading to end-stage renal disease. Animal models have been widely used to study the pathogenesis of DKD and evaluate potential therapies. However, current animal models often fail to fully capture the pathological characteristics of renal injury observed in clinical patients with DKD. Additionally, modeling DKD is often a time-consuming, costly, and labor-intensive process. The current review aims to summarize modeling strategies in the establishment of DKD animal models by utilizing meta-analysis related methods and to aid in the optimization of these models for future research. A total of 1215 articles were retrieved with the keywords of "diabetic kidney disease" and "animal experiment" in the past 10 years. Following screening, 84 articles were selected for inclusion in the meta-analysis. Review manager 5.4.1 was employed to analyze the changes in blood glucose, glycosylated hemoglobin, total cholesterol, triglyceride, serum creatinine, blood urea nitrogen, and urinary albumin excretion rate in each model. Renal lesions shown in different models that were not suitable to be included in the meta-analysis were also extensively discussed. The above analysis suggested that combining various stimuli or introducing additional renal injuries to current models would be a promising avenue to overcome existing challenges and limitations. In conclusion, our review article provides an in-depth analysis of the limitations in current DKD animal models and proposes strategies for improving the accuracy and reliability of these models that will inspire future research efforts in the DKD research field.
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Affiliation(s)
- Fanghong Li
- School of Chinese Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Zhi Ma
- School of Life SciencesBeijing University of Chinese MedicineBeijingChina
| | - Yajie Cai
- School of Chinese Materia MedicaBeijing University of Chinese MedicineBeijingChina
| | - Jingwei Zhou
- Department of Nephrology, Dongzhimen HospitalThe First Affiliated Hospital of Beijing University of Chinese MedicineBeijingChina
| | - Runping Liu
- School of Chinese Materia MedicaBeijing University of Chinese MedicineBeijingChina
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2
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Massy ZA, Lambert O, Metzger M, Sedki M, Chaubet A, Breuil B, Jaafar A, Tack I, Nguyen-Khoa T, Alves M, Siwy J, Mischak H, Verbeke F, Glorieux G, Herpe YE, Schanstra JP, Stengel B, Klein J. Machine Learning-Based Urine Peptidome Analysis to Predict and Understand Mechanisms of Progression to Kidney Failure. Kidney Int Rep 2023; 8:544-555. [PMID: 36938091 PMCID: PMC10014385 DOI: 10.1016/j.ekir.2022.11.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
Introduction The identification of patients with chronic kidney disease (CKD) at risk of progressing to kidney failure (KF) is important for clinical decision-making. In this study we assesed whether urinary peptidome (UP) analysis may help classify patients with CKD and improve KF risk prediction. Methods The UP was analyzed using capillary electrophoresis coupled to mass spectrometry in a case-cohort sample of 1000 patients with CKD stage G3 to G5 from the French CKD-Renal Epidemiology and Information Network (REIN) cohort. We used unsupervised and supervised machine learning to classify patients into homogenous UP clusters and to predict 3-year KF risk with UP, respectively. The predictive performance of UP was compared with the KF risk equation (KFRE), and evaluated in an external cohort of 326 patients. Results More than 1000 peptides classified patients into 3 clusters with different CKD severities and etiologies at baseline. Peptides with the highest discriminative power for clustering were fragments of proteins involved in inflammation and fibrosis, highlighting those derived from α-1-antitrypsin, a major acute phase protein with anti-inflammatory and antiapoptotic properties, as the most significant. We then identified a set of 90 urinary peptides that predicted KF with a c-index of 0.83 (95% confidence interval [CI]: 0.81-0.85) in the case-cohort and 0.89 (0.83-0.94) in the external cohort, which were close to that estimated with the KFRE (0.85 [0.83-0.87]). Combination of UP with KFRE variables did not further improve prediction. Conclusion This study shows the potential of UP analysis to uncover new pathophysiological CKD progression pathways and to predict KF risk with a performance equal to that of the KFRE.
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Affiliation(s)
- Ziad A. Massy
- Centre for Research in Epidemiology and Population Health, University Paris-Saclay, University Versailles-Saint Quentin, Inserm UMRS 1018, Clinical Epidemiology Team, Villejuif, France
- Department of Nephrology, CHU Ambroise Paré, APHP, Boulogne Billancourt Cedex, France
| | - Oriane Lambert
- Centre for Research in Epidemiology and Population Health, University Paris-Saclay, University Versailles-Saint Quentin, Inserm UMRS 1018, Clinical Epidemiology Team, Villejuif, France
| | - Marie Metzger
- Centre for Research in Epidemiology and Population Health, University Paris-Saclay, University Versailles-Saint Quentin, Inserm UMRS 1018, Clinical Epidemiology Team, Villejuif, France
| | - Mohammed Sedki
- Centre for Research in Epidemiology and Population Health, University Paris-Saclay, University Versailles-Saint Quentin, Inserm UMRS 1018, Methodology Pole, Villejuif, France
| | - Adeline Chaubet
- Institut National de la Santé et de la Recherche Médicale, Institute of Cardiovascular and Metabolic Disease, UMRS 1297, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale, Institute of Cardiovascular and Metabolic Disease, UMRS 1297, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Acil Jaafar
- Department of Clinical Physiology, Toulouse-Rangueil University Hospital, Toulouse University School of Medicine, Toulouse, France
| | - Ivan Tack
- Department of Clinical Physiology, Toulouse-Rangueil University Hospital, Toulouse University School of Medicine, Toulouse, France
| | - Thao Nguyen-Khoa
- Laboratory of Biochemistry, HU Necker-Enfants Malades, AP-HP Centre Université de Paris, Paris, France
- INSERM U1151, Institut Necker-Enfants Malades, Université de Paris Cité, Paris, France
| | - Melinda Alves
- Institut National de la Santé et de la Recherche Médicale, Institute of Cardiovascular and Metabolic Disease, UMRS 1297, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, 30659 Hannover, Germany
| | | | - Francis Verbeke
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, Ghent, Belgium
| | - Griet Glorieux
- Department of Internal Medicine and Pediatrics, Nephrology Section, Ghent University Hospital, Ghent, Belgium
| | - Yves-Edouard Herpe
- Biobanque de Picardie, Biological Resource Center of the Amiens University Hospital, 1 rondpoint du Pr Christian Cabrol, Amiens Cedex, France
| | - Joost P. Schanstra
- Institut National de la Santé et de la Recherche Médicale, Institute of Cardiovascular and Metabolic Disease, UMRS 1297, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Bénédicte Stengel
- Centre for Research in Epidemiology and Population Health, University Paris-Saclay, University Versailles-Saint Quentin, Inserm UMRS 1018, Clinical Epidemiology Team, Villejuif, France
- Department of Nephrology, CHU Ambroise Paré, APHP, Boulogne Billancourt Cedex, France
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale, Institute of Cardiovascular and Metabolic Disease, UMRS 1297, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
- Correspondence: Julie Klein, Institute of Metabolic and Cardiovascular disease, 1 avenue Jean-Poulhès, 31432 Toulouse Cedex 4, France.
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3
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Wei L, Han Y, Tu C. Molecular Pathways of Diabetic Kidney Disease Inferred from Proteomics. Diabetes Metab Syndr Obes 2023; 16:117-128. [PMID: 36760602 PMCID: PMC9842482 DOI: 10.2147/dmso.s392888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 12/06/2022] [Indexed: 01/18/2023] Open
Abstract
Diabetic kidney disease (DKD) affects an estimated 20-40% of type 2 diabetes patients and is among the most prevalent microvascular complications in this patient population, contributing to high morbidity and mortality rates. Currently, changes in albuminuria status are thought to be a primary indicator of the onset or progression of DKD, yet progressive nephropathy and renal impairment can occur in certain diabetic individuals who exhibit normal urinary albumin levels, emphasizing the lack of sensitivity and specificity associated with the use of albuminuria as a biomarker for detecting diabetic kidney disease and predicting DKD risk. According to the study, a non-invasive method for early detection or prediction of DKD may involve combining proteomic analytical techniques such second generation sequencing, mass spectrometry, two-dimensional gel electrophoresis, and other advanced system biology algorithms. Another category of proteins of relevance may now be provided by renal tissue biomarkers. The establishment of reliable proteomic biomarkers of DKD represents a novel approach to improving the diagnosis, prognostic evaluation, and treatment of affected patients. In the present review, a series of protein biomarkers that have been characterized to date are discussed, offering a theoretical foundation for future efforts to aid patients suffering from this debilitating microvascular complication.
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Affiliation(s)
- Lan Wei
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming, People’s Republic of China
| | - Chao Tu
- Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, People’s Republic of China
- Correspondence: Chao Tu, Department of Internal Medicine, The Third Affiliated Hospital of Soochow University, 185 Juqian Road, Changzhou, 213000, People’s Republic of China, Email
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4
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Sanchez-Martin I, Magalhães P, Ranjzad P, Fatmi A, Richard F, Manh TPV, Saurin AJ, Feuillet G, Denis C, Woolf AS, Schanstra JP, Zürbig P, Caubit X, Fasano L. Haploinsufficiency of the mouse Tshz3 gene leads to kidney defects. Hum Mol Genet 2021; 31:1921-1945. [PMID: 34919690 DOI: 10.1093/hmg/ddab362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 11/14/2022] Open
Abstract
Renal tract defects and autism spectrum disorder (ASD) deficits represent the phenotypic core of the 19q12 deletion syndrome caused by the loss of one copy of the TSHZ3 gene. While a proportion of Tshz3 heterozygous (Tshz3+/lacZ) mice display ureteral defects, no kidney defects have been reported in these mice. The purpose of this study was to characterize the expression of Tshz3 in adult kidney as well as the renal consequences of embryonic haploinsufficiency of Tshz3 by analyzing the morphology and function of Tshz3 heterozygous adult kidney. Here, we described Tshz3 expression in the smooth muscle and stromal cells lining the renal pelvis, the papilla and glomerular endothelial cells (GEnCs) of the adult kidney as well as in the proximal nephron tubules in neonatal mice. Histological analysis showed that Tshz3+/lacZ adult kidney had an average of 29% fewer glomeruli than wild type kidney. Transmission electron microscopy (TEM) of Tshz3+/lacZ glomeruli revealed a reduced thickness of the glomerular basement membrane and a larger foot process width. Compared to wild type, Tshz3+/lacZ mice showed lower blood urea, phosphates, magnesium and potassium at 2 months of age. At the molecular level, transcriptome analysis identified differentially expressed genes related to inflammatory processes in Tshz3+/lacZ compare to wild type (WT; control) adult kidneys. Lastly, analysis of the urinary peptidome revealed 33 peptides associated with Tshz3+/lacZ adult mice. These results provide the first evidence that in the mouse Tshz3 haploinsufficiency leads to cellular, molecular and functional abnormalities in the adult mouse kidney.
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Affiliation(s)
| | | | - Parisa Ranjzad
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK
| | - Ahmed Fatmi
- Aix Marseille Univ, CNRS, IBDM, UMR7288, Marseille, France
| | | | - Thien Phong Vu Manh
- Aix Marseille Univ, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | | | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, UK.,Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1297, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | - Xavier Caubit
- Aix Marseille Univ, CNRS, IBDM, UMR7288, Marseille, France
| | - Laurent Fasano
- Aix Marseille Univ, CNRS, IBDM, UMR7288, Marseille, France
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5
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Latosinska A, Siwy J, Faguer S, Beige J, Mischak H, Schanstra JP. Value of Urine Peptides in Assessing Kidney and Cardiovascular Disease. Proteomics Clin Appl 2021; 15:e2000027. [PMID: 32710812 DOI: 10.1002/prca.202000027] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/18/2020] [Indexed: 12/14/2022]
Abstract
Urinary peptides gained significant attention as potential biomarkers especially in the context of kidney and cardiovascular disease. In this manuscript the recent literature since 2015 on urinary peptide investigation in human kidney and cardiovascular disease is reviewed. The technology most commonly used in this context is capillary electrophoresis coupled mass spectrometry, in part owed to the large database available and the well-defined dataspace. Several studies based on over 1000 subjects are reported in the recent past, especially examining CKD273, a classifier for assessment of chronic kidney disease based on 273 urine peptides. Interestingly, the most abundant urinary peptides are generally collagen fragments, which may have gone undetected for some time as they are typically modified via proline hydroxylation. The data available suggest that urinary peptides specifically depict inflammation and fibrosis, and may serve as a non-invasive tool to assess fibrosis, which appears to be a key driver in kidney and cardiovascular disease. The recent successful completion of the first urinary peptide guided intervention trial, PRIORITY, is expected to further spur clinical application of urinary peptidomics, aiming especially at early detection of chronic diseases, prediction of progression, and prognosis of drug response.
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Affiliation(s)
| | - Justyna Siwy
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Stanislas Faguer
- Département de Néphrologie et Transplantation d'organes, Centre de référence des maladies rénales rares, Centre Hospitalier Universitaire de Toulouse, 1, Avenue Jean Poulhes, Toulouse, 31059, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France
- Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
| | - Joachim Beige
- Department of Nephrology and Kuratorium for Dialysis and Transplantation Renal Unit, Hospital St Georg, Delitzscher Str. 141, 04129, Leipzig, Germany
- Department of Nephrology, Martin-Luther-University Halle/Wittenberg, Universitätsplatz 10, 06108, Halle (Saale), Germany
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Rotenburger Straße 20, 30659, Hannover, Germany
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, 1 Avenue Jean Poulhès, BP 84225, Toulouse Cedex 4, 31432, France
- Université Toulouse III Paul-Sabatier, Route de Narbonne, Toulouse, 31330, France
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6
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Rinschen MM, Saez-Rodriguez J. The tissue proteome in the multi-omic landscape of kidney disease. Nat Rev Nephrol 2020; 17:205-219. [PMID: 33028957 DOI: 10.1038/s41581-020-00348-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2020] [Indexed: 02/07/2023]
Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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7
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Klein J, Caubet C, Camus M, Makridakis M, Denis C, Gilet M, Feuillet G, Rascalou S, Neau E, Garrigues L, Thillaye du Boullay O, Mischak H, Monsarrat B, Burlet-Schiltz O, Vlahou A, Saulnier-Blache JS, Bascands JL, Schanstra JP. Connectivity mapping of glomerular proteins identifies dimethylaminoparthenolide as a new inhibitor of diabetic kidney disease. Sci Rep 2020; 10:14898. [PMID: 32913274 PMCID: PMC7484761 DOI: 10.1038/s41598-020-71950-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 08/18/2020] [Indexed: 01/09/2023] Open
Abstract
While blocking the renin angiotensin aldosterone system (RAAS) has been the main therapeutic strategy to control diabetic kidney disease (DKD) for many years, 25-30% of diabetic patients still develop the disease. In the present work we adopted a systems biology strategy to analyze glomerular protein signatures to identify drugs with potential therapeutic properties in DKD acting through a RAAS-independent mechanism. Glomeruli were isolated from wild type and type 1 diabetic (Ins2Akita) mice treated or not with the angiotensin-converting enzyme inhibitor (ACEi) ramipril. Ramipril efficiently reduced the urinary albumin/creatine ratio (ACR) of Ins2Akita mice without modifying DKD-associated renal-injuries. Large scale quantitative proteomics was used to identify the DKD-associated glomerular proteins (DKD-GPs) that were ramipril-insensitive (RI-DKD-GPs). The raw data are publicly available via ProteomeXchange with identifier PXD018728. We then applied an in silico drug repurposing approach using a pattern-matching algorithm (Connectivity Mapping) to compare the RI-DKD-GPs's signature with a collection of thousands of transcriptional signatures of bioactive compounds. The sesquiterpene lactone parthenolide was identified as one of the top compounds predicted to reverse the RI-DKD-GPs's signature. Oral treatment of 2 months old Ins2Akita mice with dimethylaminoparthenolide (DMAPT, a water-soluble analogue of parthenolide) for two months at 10 mg/kg/d by gavage significantly reduced urinary ACR. However, in contrast to ramipril, DMAPT also significantly reduced glomerulosclerosis and tubulointerstitial fibrosis. Using a system biology approach, we identified DMAPT, as a compound with a potential add-on value to standard-of-care ACEi-treatment in DKD.
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Affiliation(s)
- Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Cécile Caubet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
- Evotec (France) SAS, Toulouse, France
| | - Mylène Camus
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
| | - Manousos Makridakis
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Marion Gilet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Simon Rascalou
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Eric Neau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Luc Garrigues
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
- Evotec (France) SAS, Toulouse, France
| | | | | | - Bernard Monsarrat
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), UPS, CNRS, Université de Toulouse, Toulouse, France
| | - Antonia Vlahou
- Biotechnology Laboratory, Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jean Sébastien Saulnier-Blache
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.
- Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1188 - Université de La Réunion, Saint-Denis, France.
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.
- Université Toulouse III Paul-Sabatier, Toulouse, France.
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8
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Vinel C, Schanstra JP, Boizard F, Péreira O, Auriau J, Dortignac A, Breuil B, Feuillet G, Nkuipou-Kenfack E, Zürbig P, Valet P, Bascands JL, Dray C, Denis C. Apelin affects the mouse aging urinary peptidome with minimal effects on kidney. Sci Rep 2019; 9:10647. [PMID: 31337837 PMCID: PMC6650410 DOI: 10.1038/s41598-019-47109-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 07/09/2019] [Indexed: 12/27/2022] Open
Abstract
Kidney function is altered by age together with a declined filtration capacity of 5–10% per decade after 35 years. Renal aging shares many characteristics with chronic kidney disease. Plasma levels of the bioactive peptide apelin also decline with age and apelin has been shown to be protective in chronic kidney disease. Therefore we evaluated whether apelin could also improve aging-induced renal lesions and function in mice. Since urine is for the major part composed of proteins and peptides originating from the kidney, we first studied apelin-induced changes, in the aging urinary peptidome. Despite the recently published age-associated plasma decrease of apelin, expression of the peptide and its receptor was increased in the kidneys of 24 months old mice. Twenty-eight days treatment with apelin significantly modified the urinary peptidome of 3 and 24 months old mice towards a signature suggesting more advanced age at 3 months, and a younger age at 24 months. The latter was accompanied by a decreased staining of collagen (Sirius red staining) in 24 months old apelin-treated mice, without changing aging-induced glomerular hypertrophy. In addition, apelin was without effect on aging-induced renal autophagy, apoptosis, inflammation and reduced renal function. In conclusion, treatment of aged mice with apelin had a limited effect on kidney lesions although modifying the urinary peptidome towards a younger signature. This supports evidence of apelin inducing more general beneficial effects on other aging organs, muscles in particular, as recently shown for sarcopenia, markers of which end up via the glomerular filtration in urine.
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Affiliation(s)
- Claire Vinel
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Franck Boizard
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Ophélie Péreira
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Johanna Auriau
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Alizée Dortignac
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Benjamin Breuil
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Guylène Feuillet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | | | | | - Philippe Valet
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jean-Loup Bascands
- Institut National de la Sante et de la Recherche Medicale (INSERM), U1188 - Université de La Réunion, Saint-Denis, France
| | - Cédric Dray
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Toulouse, France.
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France. .,Université Toulouse III Paul-Sabatier, Toulouse, France.
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9
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Abstract
Proteome analysis has been applied in multiple studies in the context of chronic kidney disease, aiming at improving our knowledge on the molecular pathophysiology of the disease. The approach is generally based on the hypothesis that proteins are key in maintaining kidney function, and disease is a clinical consequence of a significant change of the protein level. Knowledge on critical proteins and their alteration in disease should in turn enable identification of ideal biomarkers that could guide patient management. In addition, all drugs currently employed target proteins. Hence, proteome analysis also promises to enable identifying the best suited therapeutic target, and, in combination with biomarkers, could be used as the rationale basis for personalized intervention. To assess the current status of proteome analysis in the context of CKD, we present the results of a systematic review, of up-to-date scientific research, and give an outlook on the developments that can be expected in near future. Based on the current literature, proteome analysis has already seen implementation in the management of CKD patients, and it is expected that this approach, also supported by the positive results generated to date, will see advanced high-throughput application.
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10
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Latosinska A, Siwy J, Mischak H, Frantzi M. Peptidomics and proteomics based on CE‐MS as a robust tool in clinical application: The past, the present, and the future. Electrophoresis 2019; 40:2294-2308. [DOI: 10.1002/elps.201900091] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/16/2019] [Accepted: 04/16/2019] [Indexed: 12/23/2022]
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11
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Wu Y, Han M, Wang Y, Gao Y, Cui X, Xu P, Ji C, Zhong T, You L, Zeng Y. A Comparative Peptidomic Characterization of Cultured Skeletal Muscle Tissues Derived From db/db Mice. Front Endocrinol (Lausanne) 2019; 10:741. [PMID: 31736878 PMCID: PMC6828820 DOI: 10.3389/fendo.2019.00741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/19/2022] Open
Abstract
As an important secretory organ, skeletal muscle has drawn attention as a potential target tissue for type 2 diabetic mellitus (T2DM). Recent peptidomics approaches have been applied to identify secreted peptides with potential bioactive. However, comprehensive analysis of the secreted peptides from skeletal muscle tissues of db/db mice and elucidation of their possible roles in insulin resistance remains poorly characterized. Here, we adopted a label-free discovery using liquid chromatography tandem mass spectrometry (LC-MS/MS) technology and identified 63 peptides (42 up-regulated peptides and 21 down-regulated peptides) differentially secreted from cultured skeletal muscle tissues of db/db mice. Analysis of relative molecular mass (Mr), isoelectric point (pI) and distribution of Mr vs pI of differentially secreted peptides presented the general feature. Furthermore, Gene ontology (GO) and pathway analyses for the parent proteins made a comprehensive functional assessment of these differential peptides, indicating the enrichment in glycolysis/gluconeogenesis and striated muscle contraction processes. Intercellular location analysis pointed out most precursor proteins of peptides were cytoplasmic or cytoskeletal. Additionally, cleavage site analysis revealed that Lysine (N-terminal)-Alanine (C-terminal) and Lysine (N-terminal)-Leucine (C-terminal) represents the preferred cleavage sites for identified peptides and proceeding peptides respectively. Mapped to the precursors' sequences, most identified peptides were observed cleaved from creatine kinase m-type (KCRM) and fructose-bisphosphate aldolase A (Aldo A). Based on UniProt and Pfam database for specific domain structure or motif, 44 peptides out of total were positioned in the functional motif or domain from their parent proteins. Using C2C12 myotubes as cell model in vitro, we found several candidate peptides displayed promotive or inhibitory effects on insulin and mitochondrial-related pathways by an autocrine manner. Taken together, this study will encourage us to investigate the biologic functions and the potential regulatory mechanism of these secreted peptides from skeletal muscle tissues, thus representing a promising strategy to treat insulin resistance as well as the associated metabolic disorders.
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Affiliation(s)
- Yanting Wu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Affiliated Maternity and Child Health Care Hospital of Nantong University, NanTong, China
| | - Mei Han
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yan Wang
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Yao Gao
- Department of Endocrinology, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xianwei Cui
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Pengfei Xu
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Chenbo Ji
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Tianying Zhong
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lianghui You
- Nanjing Maternity and Child Health Care Institute, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- *Correspondence: Lianghui You
| | - Yu Zeng
- Department of Clinical Laboratory, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
- Yu Zeng
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12
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Klein J, Schanstra JP. Implementation of Proteomics Biomarkers in Nephrology: From Animal Models to Human Application? Proteomics Clin Appl 2018; 13:e1800089. [PMID: 30334380 DOI: 10.1002/prca.201800089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 10/09/2018] [Indexed: 12/20/2022]
Abstract
Preclinical animal models are extensively used in nephrology. In this review, the utility of performing proteome analysis of kidney tissue or urine in such models and transfer of the results to human application has been assessed. Analysis of the literature identified 68 relevant publications. Pathway analysis of the reported proteins clearly indicated links with known biological processes in kidney disease providing validation of the observed changes in the preclinical models. However, although most studies focused on the identification of early markers of kidney disease or prediction of its progression, none of the identified makers has made it to substantial validation in the clinic or at least in human samples. Especially in renal disease where urine is an abundant source of biomarkers of diseases of the kidney and the urinary tract, it therefore appears that the focus should be on human material based discovery studies. In contrast, the most valid information of proteome analysis of preclinical models in nephrology for translation in human disease resides in studies focusing on drug evaluation, both efficacy for translation to the clinic and for mechanistic insight.
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Affiliation(s)
- Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France.,Université Toulouse III Paul-Sabatier, Toulouse, France
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13
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Magalhães P, Pontillo C, Pejchinovski M, Siwy J, Krochmal M, Makridakis M, Carrick E, Klein J, Mullen W, Jankowski J, Vlahou A, Mischak H, Schanstra JP, Zürbig P, Pape L. Comparison of Urine and Plasma Peptidome Indicates Selectivity in Renal Peptide Handling. Proteomics Clin Appl 2018; 12:e1700163. [DOI: 10.1002/prca.201700163] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Pedro Magalhães
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
| | - Claudia Pontillo
- Department of Toxicology and Pharmacology; Hannover Medical School; 30625 Hannover Germany
| | | | - Justyna Siwy
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | | | - Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Emma Carrick
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Julie Klein
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joachim Jankowski
- RWTH Aachen University Hospital; 52074 Aachen Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht; University of Maastricht; 6211 Maastricht The Netherlands
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joost P. Schanstra
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - Petra Zürbig
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | - Lars Pape
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
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14
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Liu Y, Pejchinovski M, Wang X, Fu X, Castelletti D, Watnick TJ, Arcaro A, Siwy J, Mullen W, Mischak H, Serra AL. Dual mTOR/PI3K inhibition limits PI3K-dependent pathways activated upon mTOR inhibition in autosomal dominant polycystic kidney disease. Sci Rep 2018; 8:5584. [PMID: 29615724 PMCID: PMC5882886 DOI: 10.1038/s41598-018-22938-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 02/27/2018] [Indexed: 12/17/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is characterized by the development of kidney cysts leading to kidney failure in adulthood. Inhibition of mammalian target of rapamycin (mTOR) slows polycystic kidney disease (PKD) progression in animal models, but randomized controlled trials failed to prove efficacy of mTOR inhibitor treatment. Here, we demonstrate that treatment with mTOR inhibitors result in the removal of negative feedback loops and up-regulates pro-proliferative phosphatidylinositol 3-kinase (PI3K)-Akt and PI3K-extracellular signal-regulated kinase (ERK) signaling in rat and mouse PKD models. Dual mTOR/PI3K inhibition with NVP-BEZ235 abrogated these pro-proliferative signals and normalized kidney morphology and function by blocking proliferation and fibrosis. Our findings suggest that multi-target PI3K/mTOR inhibition may represent a potential treatment for ADPKD.
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Affiliation(s)
- Yang Liu
- Institute of Physiology, University of Zürich, Zürich, Switzerland.,Department of Biomedicine, Cancer Immunology Laboratory, University Hospital Basel, Basel, Switzerland
| | | | - Xueqi Wang
- Department of Nephrology, Second Military Medical University, Shanghai, China
| | - Xuebin Fu
- Department of Chemistry and Applied Biosciences, Molecular Pharmacology Unit, Swiss Federal Institute of Technology Zürich, Zürich, Switzerland
| | | | - Terry J Watnick
- Division of Nephrology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Alexandre Arcaro
- Department of Clinical Research, University of Bern, Bern, Switzerland
| | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hanover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Andreas L Serra
- Epidemiology, Biostatistics and Prevention Institute, University of Zürich, and Suisse ADPKD, Klinik Hirslanden Zürich, Switzerland.
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15
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Quantitative peptidomics of endogenous peptides involved in TGF-β1-induced epithelial mesenchymal transition of renal epithelial cells. Cell Death Discov 2018. [PMID: 29531806 PMCID: PMC5841401 DOI: 10.1038/s41420-017-0001-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
TGF-β1 is a key fibrotic factor mediating epithelial mesenchymal transition (EMT) of epithelial cells through various signaling pathways. However, roles of proteolytic cleavage and endogenous peptide dynamics in TGF-β1-induced EMT remain unknown. We therefore performed quantitative peptidomics of TGF-β1-induced EMT in renal tubular epithelial cells. The acquired mesenchymal characteristics were confirmed, including morphological change (from cobblestone-like to fibroblast-like), decreased epithelial marker (ZO-1), and increased mesenchymal marker (vimentin). Quantitative peptidomics using stable isotope labeling revealed significantly altered levels of 70 unique endogenous peptides (derived from internal and C-terminal parts of 39 unique precursor proteins) after EMT induction. Interestingly, the majority of these peptides were derived from non-short-lived proteins, and analysis of P1 position revealed predominance of hydrophobic residues, suggesting that these endogenous peptides were generated mainly from proteasome cleavage. This hypothesis was confirmed by treating the cells with MG132 (a proteasome inhibitor), which provided almost identical endogenous peptide pattern as of the TGF-β1-treated cells. Moreover, validation assay showed marked reduction of proteasome peptidase activity in both TGF-β1-treated and MG132-treated cells. This is the first peptidome dataset that provides several novel aspects of mechanisms for TGF-β1-induced EMT. Our data also suggest that TGF-β1 exerts inhibitory effect against proteasome activity during EMT induction.
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16
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Krochmal M, Schanstra JP, Mischak H. Urinary peptidomics in kidney disease and drug research. Expert Opin Drug Discov 2017; 13:259-268. [DOI: 10.1080/17460441.2018.1418320] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Magdalena Krochmal
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, Greece
- Mosaiques Diagnostics GmbH, Hannover, Germany
| | - Joost P Schanstra
- Institut of Cardiovascular and Metabolic Disease, Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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17
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Magalhães P, Pejchinovski M, Markoska K, Banasik M, Klinger M, Švec-Billá D, Rychlík I, Rroji M, Restivo A, Capasso G, Bob F, Schiller A, Ortiz A, Perez-Gomez MV, Cannata P, Sanchez-Niño MD, Naumovic R, Brkovic V, Polenakovic M, Mullen W, Vlahou A, Zürbig P, Pape L, Ferrario F, Denis C, Spasovski G, Mischak H, Schanstra JP. Association of kidney fibrosis with urinary peptides: a path towards non-invasive liquid biopsies? Sci Rep 2017; 7:16915. [PMID: 29208969 PMCID: PMC5717105 DOI: 10.1038/s41598-017-17083-w] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Chronic kidney disease (CKD) is a prevalent cause of morbidity and mortality worldwide. A hallmark of CKD progression is renal fibrosis characterized by excessive accumulation of extracellular matrix (ECM) proteins. In this study, we aimed to investigate the correlation of the urinary proteome classifier CKD273 and individual urinary peptides with the degree of fibrosis. In total, 42 kidney biopsies and urine samples were examined. The percentage of fibrosis per total tissue area was assessed in Masson trichrome stained kidney tissues. The urinary proteome was analysed by capillary electrophoresis coupled to mass spectrometry. CKD273 displayed a significant and positive correlation with the degree of fibrosis (Rho = 0.430, P = 0.0044), while the routinely used parameters (glomerular filtration rate, urine albumin-to-creatinine ratio and urine protein-to-creatinine ratio) did not (Rho = -0.222; -0.137; -0.070 and P = 0.16; 0.39; 0.66, respectively). We identified seven fibrosis-associated peptides displaying a significant and negative correlation with the degree of fibrosis. All peptides were collagen fragments, suggesting that these may be causally related to the observed accumulation of ECM in the kidneys. CKD273 and specific peptides are significantly associated with kidney fibrosis; such an association could not be detected by other biomarkers for CKD. These non-invasive fibrosis-related biomarkers can potentially be implemented in future trials.
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Affiliation(s)
- Pedro Magalhães
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Katerina Markoska
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
| | - Miroslaw Banasik
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Marian Klinger
- Department of Nephrology and Transplantation Medicine, Wroclaw Medical University, Wroclaw, Poland
| | - Dominika Švec-Billá
- 1st Department of Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Ivan Rychlík
- 1st Department of Medicine, Third Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Merita Rroji
- Department of Nephrology, University Hospital Center "Mother Teresa", Tirana, Albania
| | - Arianna Restivo
- Department of Nephrology, University of Campania "Luigi Vanvitelli", Naples, Italy
| | | | - Flaviu Bob
- Department of Nephrology, 'Victor Babes' University of Medicine and Pharmacy, County Emergency Hospital, Timisoara, Romania
| | - Adalbert Schiller
- Department of Nephrology, 'Victor Babes' University of Medicine and Pharmacy, County Emergency Hospital, Timisoara, Romania
| | | | | | | | | | - Radomir Naumovic
- Clinic of Nephrology, Clinical Center of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Voin Brkovic
- Clinic of Nephrology, Clinical Center of Serbia, Belgrade, Serbia
- School of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | | | - Lars Pape
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Goce Spasovski
- Department of Nephrology, Medical Faculty, University of Skopje, Skopje, Macedonia
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Cardiovascular and Metabolic Disease, Toulouse, France.
- Université Toulouse III Paul-Sabatier, Toulouse, France.
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18
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Krochmal M, Kontostathi G, Magalhães P, Makridakis M, Klein J, Husi H, Leierer J, Mayer G, Bascands JL, Denis C, Zoidakis J, Zürbig P, Delles C, Schanstra JP, Mischak H, Vlahou A. Urinary peptidomics analysis reveals proteases involved in diabetic nephropathy. Sci Rep 2017; 7:15160. [PMID: 29123184 PMCID: PMC5680307 DOI: 10.1038/s41598-017-15359-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 10/24/2017] [Indexed: 12/13/2022] Open
Abstract
Mechanisms underlying the onset and progression of nephropathy in diabetic patients are not fully elucidated. Deregulation of proteolytic systems is a known path leading to disease manifestation, therefore we hypothesized that proteases aberrantly expressed in diabetic nephropathy (DN) may be involved in the generation of DN-associated peptides in urine. We compared urinary peptide profiles of DN patients (macroalbuminuric, n = 121) to diabetic patients with no evidence of DN (normoalbuminuric, n = 118). 302 sequenced, differentially expressed peptides (adjusted p-value < 0.05) were analysed with the Proteasix tool predicting proteases potentially involved in their generation. Activity change was estimated based on the change in abundance of the investigated peptides. Predictions were correlated with transcriptomics (Nephroseq) and relevant protein expression data from the literature. This analysis yielded seventeen proteases, including multiple forms of MMPs, cathepsin D and K, kallikrein 4 and proprotein convertases. The activity of MMP-2 and MMP-9, predicted to be decreased in DN, was investigated using zymography in a DN mouse model confirming the predictions. Collectively, this proof-of-concept study links urine peptidomics to molecular changes at the tissue level, building hypotheses for further investigation in DN and providing a workflow with potential applications to other diseases.
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Affiliation(s)
| | | | - Pedro Magalhães
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Department of Pediatric Nephrology, Hannover Medical School, Hannover, Germany
| | | | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Holger Husi
- Department of Diabetes and Cardiovascular Science, University of the Highlands and Islands, Centre for Health Science, Inverness, IV2 3JH, UK
| | - Johannes Leierer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Gert Mayer
- Department of Internal Medicine IV (Nephrology and Hypertension), Medical University Innsbruck, Innsbruck, Austria
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1188 - Université de La, Réunion, France
| | - Colette Denis
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Jerome Zoidakis
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France
- Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Harald Mischak
- Mosaiques Diagnostics GmbH, Hannover, Germany
- Institute of Cardiovascular and Medical Sciences, BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow, G12 8TA, UK
| | - Antonia Vlahou
- Biomedical Research Foundation Academy of Athens, Athens, Greece.
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19
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Pontillo C, Mischak H. Urinary peptide-based classifier CKD273: towards clinical application in chronic kidney disease. Clin Kidney J 2017; 10:192-201. [PMID: 28694965 PMCID: PMC5499684 DOI: 10.1093/ckj/sfx002] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Indexed: 12/22/2022] Open
Abstract
Capillary electrophoresis coupled with mass spectrometry (CE-MS) has been used as a platform for discovery and validation of urinary peptides associated with chronic kidney disease (CKD). CKD affects ∼ 10% of the population, with high associated costs for treatments. A urinary proteome-based classifier (CKD273) has been discovered and validated in cross-sectional and longitudinal studies to assess and predict the progression of CKD. It has been implemented in studies employing cohorts of > 1000 patients. CKD273 is commercially available as an in vitro diagnostic test for early detection of CKD and is currently being used for patient stratification in a multicentre randomized clinical trial (PRIORITY). The validity of the CKD273 classifier has recently been evaluated applying the Oxford Evidence-Based Medicine and Southampton Oxford Retrieval Team guidelines and a letter of support for CKD273 was issued by the US Food and Drug Administration. In this article we review the current evidence published on CKD273 and the challenges associated with implementation. Definition of a possible surrogate early endpoint combined with CKD273 as a biomarker for patient stratification currently appears as the most promising strategy to enable the development of effective drugs to be used at an early time point when intervention can still be effective.
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Affiliation(s)
| | - Harald Mischak
- Mosaiques Diagnostics, Hannover, Germany.,Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
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20
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The use of urinary proteomics in the assessment of suitability of mouse models for ageing. PLoS One 2017; 12:e0166875. [PMID: 28199320 PMCID: PMC5310860 DOI: 10.1371/journal.pone.0166875] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022] Open
Abstract
Ageing is a complex process characterised by a systemic and progressive deterioration of biological functions. As ageing is associated with an increased prevalence of age-related chronic disorders, understanding its underlying molecular mechanisms can pave the way for therapeutic interventions and managing complications. Animal models such as mice are commonly used in ageing research as they have a shorter lifespan in comparison to humans and are also genetically close to humans. To assess the translatability of mouse ageing to human ageing, the urinary proteome in 89 wild-type (C57BL/6) mice aged between 8–96 weeks was investigated using capillary electrophoresis coupled to mass spectrometry (CE-MS). Using age as a continuous variable, 295 peptides significantly correlated with age in mice were identified. To investigate the relevance of using mouse models in human ageing studies, a comparison was performed with a previous correlation analysis using 1227 healthy subjects. In mice and humans, a decrease in urinary excretion of fibrillar collagens and an increase of uromodulin fragments was observed with advanced age. Of the 295 peptides correlating with age, 49 had a strong homology to the respective human age-related peptides. These ortholog peptides including several collagen (N = 44) and uromodulin (N = 5) fragments were used to generate an ageing classifier that was able to discriminate the age among both wild-type mice and healthy subjects. Additionally, the ageing classifier depicted that telomerase knock-out mice were older than their chronological age. Hence, with a focus on ortholog urinary peptides mouse ageing can be translated to human ageing.
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Isaka Y. Epidermal growth factor as a prognostic biomarker in chronic kidney diseases. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:S62. [PMID: 27868030 DOI: 10.21037/atm.2016.10.64] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Yoshitaka Isaka
- Department of Nephrology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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